PhenoGazer: A high-throughput phenotyping system to track plant stress responses using hyperspectral reflectance, nighttime chlorophyll fluorescence and RGB imaging in controlled environments

Authors: HASSAN, MUHAMMAD - Oak Ridge Institute For Science And Education (ORISE); Chang, Christine

Submitted to: Plant Phenomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2025
Publication Date: 4/28/2025
Citation: Hassan, M.A., Chang, C.Y. 2025. PhenoGazer: A high-throughput phenotyping system to track plant stress responses using hyperspectral reflectance, nighttime chlorophyll fluorescence and RGB imaging in controlled environments. Plant Phenomics. 7(2):100047. https://doi.org/10.1016/j.plaphe.2025.100047.
DOI: https://doi.org/10.1016/j.plaphe.2025.100047

Interpretive Summary: Automated high-throughput phenotyping (HTP) systems are advanced tools that can be used to monitor crop performance and inform farm management and breeding applications. HTP systems have been developed for field and greenhouse use, but few have been designed for controlled-environment chamber systems where plant responses to abiotic stresses can be fully controlled to eliminate sources of variability. We thus developed PhenoGazer, an automated HTP system for controlled environments that monitors plant health and development through a combination of spectral, imaging and environmental data. We present the system hardware and software design and demonstrate an example application using soybean with different irrigation treatments. Data collected by PhenoGazer can be used to accelerate understanding of the relationships between remotely sensed signals, plant performance and environmental stresses.

Technical Abstract: High throughput phenotyping for crop monitoring at both leaf and canopy scales is essential for understanding plant responses to various stresses. PhenoGazer, a high-throughput phenotyping system, enhances crop monitoring in controlled environments by integrating a portable hyperspectral spectrometer with eight fiber optics, four Raspberry Pi cameras, and blue LED lights. This system allows for comprehensive assessment of plant health and development. PhenoGazer features automated moveable upper and lower racks for continuous measurements. The lower rack, equipped with four blue LED lights and spectrometer fiber optics, captures blue light-induced chlorophyll fluorescence at night. The upper rack, carrying four spectrometer fiber optics and cameras, captures hyperspectral reflectance and RGB images during the day. This dual capability enables detailed evaluation of plant phenology, stress responses, and growth dynamics throughout the entire crop growth cycle. Fully automated and managed by a Raspberry Pi running Python scripts, PhenoGazer ensures precise control and data acquisition with minimal human intervention. Additionally, it includes continuous measurements through a datalogger to acquire photosynthetically active radiation (PAR), soil moisture and temperature, and features expansion capability for additional analog or digital sensors as desired by end users. To test the system, soybean plants were grown under varying water and temperature treatments to monitor growth and stress responses. PhenoGazer successfully phenotyped plants under different conditions in a walk-in growth chamber. By combining chlorophyll fluorescence, hyperspectral reflectance, and RGB imaging, PhenoGazer represents a significant advancement in plant phenotyping technology, enhancing our understanding of crop responses to environmental conditions and supporting optimized crop performance in research and agricultural applications.